HiCExplorer is a powerful and easy to use set of tools to process, normalize and visualize Hi-C data.
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Updated
Dec 2, 2024 - Python
HiCExplorer is a powerful and easy to use set of tools to process, normalize and visualize Hi-C data.
Extract Sequence from Genome According to Annotation File
Software for comparing contact maps from HiC, CaptureC and other 3D genome data.
Nextflow DSL2 pipeline to generate a Genome Note, including assembly statistics, quality metrics, and Hi-C contact maps. This workflow is part of the Tree of Life production suite.
Blazing fast toolkit to work with .hic and .cool files
Joint normalization of two Hi-C matrices, visualization and detection of differential chromatin interactions. See multiHiCcompare for the analysis of multiple Hi-C matrices
High-performance stochastic modeling of DNA loop extrusion interactions
Phasing and scaffolding polyploid genomes based on Pore-C or Hi-C.
3DGB is a workflow to build 3D models of genomes from HiC data
Pipeline for HiCAR data, a robust and sensitive multi-omic co-assay for simultaneous measurement of transcriptome, chromatin accessibility and cis-regulatory chromatin contacts.
I'm sharing my automation of the 3D_DNA and SALSA Hi-C scaffolding pipelines.
FIREcaller: Python library for detecting Frequently Interacting REgions (FIREs) from Hi-C data
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